ABSTRACT: Coral reefs have recently suffered severe environmental perturbations. Genetic variability and structure in coral populations is important in determining their survival and adaptation and can be influenced by larval settlement/recruitment. Here, we assess the genetic heterogeneity of Agaricia agaricites coral recruits at 3 spatial scales on the East Flower Garden Bank, Gulf of Mexico. Racks with settlement plates were placed at each of 3 sites, at 23 m depth, arranged in a circular pattern, 10s of meters apart. Three racks were placed within each site, several meters from each other. Each rack held 5 terracotta settling plates, several centimeters apart. Highly polymorphic markers for amplified fragment length polymorphisms (AFLP) were used to assess genetic structure among recruits: among sites, racks, and plates. Four sets of AFLP primers yielded 164 polymorphic markers. The assignment-based statistical programs AFLPOP and STRUCTURE assigned coral spat back to their original sites (home populations) at levels of between 63.3 and 99.8%. Recruit populations exhibited clear, consistent genetic heterogeneity at a scale of 10s of meters. The levels of assignment back to rack home populations were broader, ranging from 32.5 to 96.5%. Highest rates of self-­assignment/identification of distinct/separate populations occurred at the smallest spatial scale, i.e. the plates (53.7 to 96.5%). Genetic relatedness among recruits was highest and patchy at a scale of 10s of centimeters, more variable at a scale of meters, and still detectable at a scale of 10s of meters. Genetic variability in these recruits was high. Recruitment was probably local, from corals in the immediate vicinity, and with limited mixing.